This is a slight modification to whosawhatsis' excellent Minimalistic X-rod mount. Thanks to whosawhatsis for including the OpenSCAD code.
I made it 2mm thicker, and extended the body out around the nuts.
I also removed the rep-rap style teardrop, because I could not see what that helped.
And of course I made the resolution really high so the files would be huge and skeinforge slow.
(plagiarized from the original)
Press the captive nut into the slot above the rod hole (tighten it onto a screw to press-fit it and make sure it's aligned), then insert the rod. Mount the clamp to the inside of the Cupcake body with four screws, then tighten down the clamping screw to lock the rod in place. You'll probably need a ball-end hex driver for this (my Makerbot came with one).
Added: You may want to use a 1/8" drill (which is 3.18mm) or a 3mm drill to clean out the holes.